Engineer agricultural soils for improved plant growth (e.g., improve nutrient content, improve physical qualities).

Engineer agricultural soil microbiomes to increase crop nutrient capture, uptake, and assimilation.

• Technical Achievement: Engineer microbiomes to produce plant hormones that encourage symbiotic growth between arbuscular mycorrhiza fungi and plant roots.
• Technical Achievement: Engineer microbiomes with enhanced microbial sequestration (e.g., of arsenic, heavy metals, soil toxins), that also facilitate metal deposition to create particles that can be easily removed from soils.
• Technical Achievement: Engineer root-associated microbiomes to enhance depleted soils by reconstituting nutrients (e.g., nitrogen) needed for plant growth.¹Van Deynze, A., Zamora, P., Delaux, P.-M., Heitmann, C., Jayaraman, D., Rajasekar, S., Graham, D., Maeda, J., Gibson, D., Schwartz, K. D., Berry, A. M., Bhatnagar, S., Jospin, G., Darling, A., Jeannotte, R., Lopez, J., Weimer, B. C., Eisen, J. A., Shapiro, H.-Y., … Bennett, A. B. (2018). Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology, 16(8), e2006352. View Publication

Engineer soil microbiomes to locally concentrate minerals and other micronutrients to improve crop nutrient content.

• Technical Achievement: Engineer soil microbiomes that increase bioavailability of nitrogen and phosphorus, regardless of plant host organism.
• Technical Achievement: Design microbiomes that concentrate nitrogen, phosphorus, potassium, vitamins, and trace minerals in root rhizosphere.
• Technical Achievement: Design microbiomes that autolyse under predetermined environmental conditions to release nutrients for plant growth.
• Technical Achievement: Engineer microbiomes that can be grown at scale and applied to agricultural soils (i.e., microbial fertilizers) to replenish nutrients that were removed during the previous growing season.

Engineer microbiomes that help improve physical characteristics of soils (e.g., texture, density, consistency, air).

• Technical Achievement: Design microbiomes that produce biofilms or heat-resistant spores to help retain water in the soil.
• Technical Achievement: Engineer synthetic soil microbiomes to produce low-cost, bio-based superabsorbents (e.g., acrylic acid-secreting microbiomes to produce water-retaining polymers) on-demand.
• Technical Achievement: Engineer microbiomes that secrete extracellular polymers to decrease erosion (e.g., wind, water).

Improve crop resistance to biotic and abiotic stresses (e.g., disease, drought, temperature, nitrogen limitation).

Engineer phyllosphere and rhizosphere microbiomes to reduce plant pathogen infections.

• Technical Achievement: Engineer microbiomes to secrete plant defense hormones (e.g., salicylic acid) in response to pathogens, so the plant is protected against pathogens without altering plant growth or yield.
• Technical Achievement: Engineer plant-associated microbiomes that produce antimicrobial compounds in response to pathogens.

Engineer plant microbiomes to increase crop drought tolerance.

• Technical Achievement: Design leaf microbiomes that produce biofilms to decrease transpiration without affecting carbon dioxide uptake.
• Technical Achievement: Engineer microbiomes that facilitate increased water capture from atmospheric moisture, in drought or heat sensitive plants.

Engineer disease suppressive soil microbiomes to improve plant health.²Schlatter, D., Kinkel, L., Thomashow, L., Weller, D., & Paulitz, T. (2017). Disease Suppressive Soils: New Insights from the Soil Microbiome. Phytopathology, 107(11), 1284–1297. View Publication

• Technical Achievement: Design microbiomes that support plant resilience during stress-inducing environmental conditions (e.g., drought, flood).
• Technical Achievement: Engineer microbiomes that express decoy cell wall components that are targeted by pathogens.
• Technical Achievement: Engineer microbiomes that secrete pathogen-specific cell-wall degrading enzymes to reduce pathogen disease pressure.

Design microbiomes that facilitate above-ground nitrogen fixation through epiphytic interactions.³Warshan, D., Espinoza, J. L., Stuart, R. K., Richter, R. A., Kim, S.-Y., Shapiro, N., Woyke, T., C Kyrpides, N., Barry, K., Singan, V., Lindquist, E., Ansong, C., Purvine, S. O., M Brewer, H., Weyman, P. D., Dupont, C. L., & Rasmussen, U. (2017). Feathermoss and epiphytic Nostoc cooperate differently: Expanding the spectrum of plant–cyanobacteria symbiosis. The ISME Journal, 11(12), 2821–2833. View Publication

• Technical Achievement: Engineer microbiomes that support symbioses between plants and microbial epiphytes, such as cyanobacteria, that are capable of fixing nitrogen.
• Technical Achievement: Engineer plant phyllosphere microbiomes to fix nitrogen via epiphytic interactions with the plant host.

Mitigate food spoilage.

Engineer microbiomes to promote preservation and reduce reliance on refrigeration for food storage.

• Technical Achievement: Engineer microbiomes to directly counteract spoilage-causing microbes.
• Technical Achievement: Engineer microbiomes to dynamically express preservatives (such as benzoate) in response to specific environmental signals (e.g., time, temperature, pH).

Engineer microbiomes to sense and report early biomarkers of food spoilage, independent of foodborne pathogens.

• Technical Achievement: Biosensors identified and integrated into a microbe which respond to spoilage-specific quorum sensing molecules.
• Technical Achievement: Engineer inert microbiomes to produce propionate to inhibit the growth of other bacteria as a preservative and to prevent food spoilage.

Engineer microbiomes to selectively release molecules that increase or decrease the speed of fruit ripening (e.g., ethylene, methyl salicylate).

• Technical Achievement: Design microbiomes that produce or breakdown ethylene in response to local concentrations (i.e., fruits ripen quickly but are slow to spoil).
• Technical Achievement: Engineer food-safe microbiomes that can be inoculated on the surface of fresh foods to prevent gas transfer via biofilm formation (i.e., to slow oxidation or prevent reactivity to exogenous ripening hormones).

Reduce spread of foodborne pathogens.

Design microbiomes to sense and report food-borne pathogens.

• Technical Achievement: Design biosensors identified and integrated into a microbe which respond to toxins and/or quorum-sensing molecules (e.g., Salmonella enterica).
• Technical Achievement: Engineer microbiomes to detect viral foodborne pathogens (e.g., Hepatitis A) and produce colorometric indicators upon detection.

Utilize engineered microbiomes to destroy environmental foodborne pathogens (e.g., Listeria monocytogenes, Clostridium spp., Campylobacter spp., Toxoplasma gondii), excluding pathogens that spread human-to-human.

• Technical Achievement: Engineer microbiomes to break down known bacterial toxins involved in food-borne pathogens (e.g., botulinum toxin).
• Technical Achievement: Engineer microbiomes to break down known virus involved in food-borne pathogens (e.g., Hepatitis A).

Develop engineered microbiomes that can be used for disease surveillance in animals.

• Technical Achievement: Engineer microbiomes that produce an easily-detected (e.g., colorimetric) and safely-excreted (e.g., through urine or feces) metabolite when dysbiosis occurs, from pathogens or noninfectious diseases.
• Technical Achievement: Engineer microbiomes that acquire and encode pathogen DNA to facilitate easier sequencing and tracking of pathogen evolution or recombination (e.g., influenza A genome segments that get stored on a plasmid).
• Technical Achievement: In vivo (i.e., in animals) sensors of zoonotic diseases to improve animal health and reduce transmission to humans.

Footnotes

1. Van Deynze, A., Zamora, P., Delaux, P.-M., Heitmann, C., Jayaraman, D., Rajasekar, S., Graham, D., Maeda, J., Gibson, D., Schwartz, K. D., Berry, A. M., Bhatnagar, S., Jospin, G., Darling, A., Jeannotte, R., Lopez, J., Weimer, B. C., Eisen, J. A., Shapiro, H.-Y., … Bennett, A. B. (2018). Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology, 16(8), e2006352. https://doi.org/10.1371/journal.pbio.2006352
2. Schlatter, D., Kinkel, L., Thomashow, L., Weller, D., & Paulitz, T. (2017). Disease Suppressive Soils: New Insights from the Soil Microbiome. Phytopathology, 107(11), 1284–1297. https://doi.org/10.1094/PHYTO-03-17-0111-RVW
3. Warshan, D., Espinoza, J. L., Stuart, R. K., Richter, R. A., Kim, S.-Y., Shapiro, N., Woyke, T., C Kyrpides, N., Barry, K., Singan, V., Lindquist, E., Ansong, C., Purvine, S. O., M Brewer, H., Weyman, P. D., Dupont, C. L., & Rasmussen, U. (2017). Feathermoss and epiphytic Nostoc cooperate differently: Expanding the spectrum of plant–cyanobacteria symbiosis. The ISME Journal, 11(12), 2821–2833. https://doi.org/10.1038/ismej.2017.134